Robert Fox (The Boy from Oz, Frost/Nixon) is producing along with del Toro and Gary Ungar.
A target season and premiere city were not revealed.
"I'm so excited about translating Guillermo's magical vision into music and songs. I'm such a longtime fan of both Guillermo and Paul that to work on this with them is truly a dream come true," Santaolalla said.
The 1944-set film centers on a young girl who escapes the rule of her cruel stepfather by venturing into a mysterious labyrinth where she encounters magical creatures.
Released in 2006, "Pan's Labyrinth" won Academy Awards for Best Art Direction, Best Cinematography and Best Makeup.